RetrogeneDB ID: retro_etel_2213

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_99283:375..842(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000009049
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL43
• Ensembl ID: ENSETEG00000012498
• Aliases: None
• Description: mitochondrial ribosomal protein L43 [Source:HGNC Symbol;Acc:14517]

Sequence

>retro_etel_2213
ATCACGGCGCGTGGGACTGCCAGCCGCTTCCTCAGGAGTGTTCTCCACAATGGCCTGGGTCGTTAAGTGCAGCAGCTGCA
GCATCTCAGCATCCCTCTCAGCCGCGACGGGCCCTTGTCCCGCGGAGCCAGGGAGTTCGTGGAACGGGAGGTGACCGACT
TCGCCTGGCGGAACCCAGGGGTCATGATTTACGTGACCCCTCGGCCATGCTGCGTGCCCACAGTGGTGGCGGAATACTTG
AACTGGGCCGTGCGCGAGGAGAGCGTCCACTGCAAGTCCCCCCAGAGATCGCCGCGCTGGTGTAGAAACTGGCCAACCAT
TCGGGCCTCGAAGTGATCCGCATCCTCAAGCCCTTCCACACAGACAACCCGAGTGTGCAGGGCCAATGGCAACCCTTCAC
CAACAAACCGACCGCGCCCGGCCGGCTGCGCCCTCGCGAGGTCGCGCCAGCCCAGGGGTCAGCGCAG

Alignment

ORF - retro_etel_2213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 63.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTARGTASRFLTSVLHNGLGRYVQQLQRLSFRLSRDGPSSCGAREFVEREVTDFARRNPGVVIYVTPRPC
          .TARGTASRFL.SVLHNGLGR.VQQLQ.LS..LSRDGP.S.GAREFVEREVTDFA.RNPGV.IYVTPRPC
Retrocopy ITARGTASRFLRSVLHNGLGR*VQQLQHLSIPLSRDGPLSRGAREFVEREVTDFAWRNPGVMIYVTPRPC

Parental  CVPTVVAEYLNGAVREESVHCKS-APEIAALVQKLANQSGLEVIRIRKPFHTDNPSVQGQWHPFTNKPTA
          CVPTVVAEYLN.AVREESVHCKS..PEIAALV.KLAN.SGLEVIRI.KPFHTDNPSVQGQW.PFTNKPTA
Retrocopy CVPTVVAEYLNWAVREESVHCKS<PPEIAALV*KLANHSGLEVIRILKPFHTDNPSVQGQWQPFTNKPTA

Parental  PGRLRPREAAPAQDPAE
          PGRLRPRE.APAQ..A.
Retrocopy PGRLRPREVAPAQGSAQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_2213 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009742	1 retrocopy	retro_cfam_1720,
Erinaceus europaeus	ENSEEUG00000004807	1 retrocopy	retro_eeur_444,
Echinops telfairi	ENSETEG00000012498	1 retrocopy	retro_etel_2213 ,
Microcebus murinus	ENSMICG00000000014	1 retrocopy	retro_mmur_370,
Macaca mulatta	ENSMMUG00000010679	1 retrocopy	retro_mmul_1882,
Nomascus leucogenys	ENSNLEG00000014812	1 retrocopy	retro_nleu_17,